Research Article
On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics
Table 2
Biological simulation tools comparison.
| Tool | Calculus | Simulation schema | Parallelism | Data analysis |
| SCWC | CWC | Gillespie | FastFlow | Online statistics | SPiM | -calculus | Gillespie | None | None | Dizzy | Reaction model | Gillespie, Gibson-Bruck, Tau-Leap, ODE | None | None | BioPEPA | Process algebra | ODE, Gillespie | None | None | Cellware | Reaction model | Gillespie, Gibson-Bruck, ODE | None | None | DiVinE | Model checker | ODE | MPI | None | StochKit | Reaction model | Gillespie, Tau-leaping | MPI | Postprocessing | StochKit2 | Reaction model | Gillespie, Tau-leaping | Multithread | Postprocessing | StochKit-FF | Reaction model | Gillespie, Tau-leaping | FastFlow | Online statistics | Hy3S | Reaction model | Gibson-Bruck, Hybrid | MPI | Postprocessing | Li and Petzold’s | Reaction model | Gillespie | GPGPU | None | StochSimGPU | Reaction model | Gillespie, Gibson-Bruck, Li | GPGPU | Postprocessing |
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